[Adephylo-commits] r186 - / pkg pkg/R pkg/man pkg/src

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Oct 31 13:23:50 CET 2012 

Author: jombart
Date: 2012-10-31 13:23:42 +0100 (Wed, 31 Oct 2012)
New Revision: 186

Modified:
   pkg.pdf
   pkg/ChangeLog
   pkg/R/abouheif.R
   pkg/R/orthogram.R
   pkg/R/ppca.R
   pkg/R/utils.R
   pkg/man/dibas.Rd
   pkg/src/distPhylo.c
   pkg/src/misc.c
   pkg/src/sptips.c
Log:
last changes for the release of 1.1-3

Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/ChangeLog	2012-10-31 12:23:42 UTC (rev 186)
@@ -1,3 +1,24 @@
+			CHANGES IN ADEPHYLO VERSION 1.1-3
+
+
+NEW FEATURES
+
+	o added dibas, a new (and still under development) method for
+	describing/testing phylogenetic clusters
+
+
+BUG FIXES
+
+	o replaced the use of .First.lib and library.dynam by more
+	up-to-date procedures
+
+	o replaced a call to a C procedure from ade4 to the same procedure
+	in adephylo
+
+	o replaced instances of 'printf' by 'Rprintf' in C procedures
+
+
+
 			CHANGES IN ADEPHYLO VERSION 1.1-1
 
 
@@ -15,7 +36,7 @@
 	o the phylogenetic Principal Component Analysis (pPCA, Jombart et
 	al. 2010) has been implemented in adephylo. See ?ppca for more
 	information.
-	
+
 	o phylogenetic distances and proximities are now computed using
 	compiled C code, speeding up dramatically computations and making
 	the functions applicable to large trees (thousands of tips).

Modified: pkg/R/abouheif.R
===================================================================
--- pkg/R/abouheif.R	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/R/abouheif.R	2012-10-31 12:23:42 UTC (rev 186)
@@ -47,7 +47,7 @@
         restot = double (nrepet),
         PACKAGE="adephylo"
     )
-    res <- as.krandtest(obs=res$obs,sim=matrix(res$result,ncol=nvar, byr=TRUE),
+    res <- as.krandtest(obs=res$obs,sim=matrix(res$result,ncol=nvar, byrow=TRUE),
                         names=test.names,alter=alter)
     return(res)
 } # end abouheif.moran

Modified: pkg/R/orthogram.R
===================================================================
--- pkg/R/orthogram.R	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/R/orthogram.R	2012-10-31 12:23:42 UTC (rev 186)
@@ -100,7 +100,7 @@
                 Dmax = double(nrepet+1),
                 SCE = double(nrepet+1),
                 ratio = double(nrepet+1),
-                PACKAGE="ade4"
+                PACKAGE="adephylo"
                 )
     } else {
         w <- .C("MVarianceDecompInOrthoBasis",
@@ -178,7 +178,7 @@
     segments(mp[1], 1/npro, mp[npro], 1, lty = 1)
     fun(w$sig975)
     fun(w$sig025)
-    arrows(mp[x0], sig50[x0], mp[x0], phylocum[x0], ang = 15, le = 0.15,
+    arrows(mp[x0], sig50[x0], mp[x0], phylocum[x0], angle = 15, length = 0.15,
            lwd = 2)
     box()
     if (missing(nclass)) {

Modified: pkg/R/ppca.R
===================================================================
--- pkg/R/ppca.R	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/R/ppca.R	2012-10-31 12:23:42 UTC (rev 186)
@@ -66,7 +66,7 @@
 
     ## computations of the ppca
     X <- as.matrix(X)
-    decomp <- eigen( ((t(X) %*% W %*% X)/N), sym=TRUE)
+    decomp <- eigen( ((t(X) %*% W %*% X)/N), symmetric=TRUE)
     U <- decomp$vectors # U: principal axes
     lambda <- decomp$values
 
@@ -413,7 +413,7 @@
     ## 3) loadings
     if(length(axes)==1){ # one axis retained
         par(mar=c(2.5,4,2,1))
-        dotchart(x$c1[,1], lab=row.names(x$c1), main="Loadings",
+        dotchart(x$c1[,1], labels=row.names(x$c1), main="Loadings",
                  cex=par("cex")*.66)
         abline(v=median(x$c1[,1]), lty=2)
         par(mar=rep(.1,4))

Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/R/utils.R	2012-10-31 12:23:42 UTC (rev 186)
@@ -91,7 +91,7 @@
     ## function pathTwoTips (takes two path-to-root as args)
     pathTwoTips <- function(path1, path2){
         cpath <- c(path1, path2)
-        temp <- factor(cpath, level=unique(cpath))
+        temp <- factor(cpath, levels=unique(cpath))
         CA <- temp[table(temp)==2][1] # most recent common ancestor (MRCA)
         CA <- as.integer(as.character(CA)) # retrieve integer type
         path1 <- path1[1:(which(path1==CA))] # cut path1 after MRCA (keep MRCA)

Modified: pkg/man/dibas.Rd
===================================================================
--- pkg/man/dibas.Rd	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/man/dibas.Rd	2012-10-31 12:23:42 UTC (rev 186)
@@ -38,6 +38,7 @@
 }
 \author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
 \examples{
+\dontrun{
 if(require(ape)){
 #### SIMPLE SIMULATED DATA ####
 ## 50 variables, 2 groups, 30 indiv
@@ -106,10 +107,9 @@
 
 plot(table(res$groups), main="Group assignment - dibas Abouheif")
 
-
 }
-
 }
+}
 
 
 

Modified: pkg/src/distPhylo.c
===================================================================
--- pkg/src/distPhylo.c	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/src/distPhylo.c	2012-10-31 12:23:42 UTC (rev 186)
@@ -17,8 +17,8 @@
 #include <R_ext/Utils.h>
 #include "adesub.h"
 #include "sptips.h"
+#include <R_ext/Print.h>
 
-
 /* 
    =============================
    UTILITARY (INTERNAL) FUNCTIONS
@@ -41,8 +41,9 @@
 	posi = intAinB(myNode, desc, N);
 
 	if(posi==0){
-		printf("\n Likely error in findedgelength: edge not found");
-		return(0.0);
+	    Rprintf("\n Likely error in findedgelength: edge not found");
+	    /* printf("\n Likely error in findedgelength: edge not found"); */
+	    return(0.0);
 	}
 
 	/* return corresponding length */
@@ -71,7 +72,8 @@
 	}
 
 	if(nbDD==0){
-		printf("\n Likely error in findNbDD: no direct descendent found.\n");
+	    Rprintf("\n Likely error in findNbDD: no direct descendent found.\n");
+	    /* printf("\n Likely error in findNbDD: no direct descendent found.\n"); */
 	}
 
 	/* return corresponding length */
@@ -182,7 +184,8 @@
 
 	 default :
 		 res=0.0;
-		 printf("\n\n Likely error in dist2tips: unknown method (%d):", method);
+		 Rprintf("\n\n Likely error in dist2tips: unknown method (%d):", method);
+		 /* printf("\n\n Likely error in dist2tips: unknown method (%d):", method); */
 		 break;
 	 }
 
@@ -224,7 +227,8 @@
 	/* check resSize */
 	temp = (*nTips) * (*nTips-1) / 2;
 	if(*resSize !=  temp) {
-		printf("\n Likely error in distalltips: resSize is %d, and should be %d.\n", *resSize, temp);
+	    Rprintf("\n Likely error in distalltips: resSize is %d, and should be %d.\n", *resSize, temp);
+	    /* printf("\n Likely error in distalltips: resSize is %d, and should be %d.\n", *resSize, temp); */
 		return;
 	}
 

Modified: pkg/src/misc.c
===================================================================
--- pkg/src/misc.c	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/src/misc.c	2012-10-31 12:23:42 UTC (rev 186)
@@ -3,6 +3,7 @@
 #include <string.h>
 #include <stdlib.h>
 #include <stdio.h>
+#include <R_ext/Print.h>
 
 /* interpolate values in a density */
 /* x contais n values for which we want y=f(x) */

Modified: pkg/src/sptips.c
===================================================================
--- pkg/src/sptips.c	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg/src/sptips.c	2012-10-31 12:23:42 UTC (rev 186)
@@ -22,6 +22,7 @@
 #include <R.h>
 #include <R_ext/Utils.h>
 #include "adesub.h"
+#include <R_ext/Print.h>
 
 
 

Modified: pkg.pdf
===================================================================
--- pkg.pdf	2012-10-31 11:27:39 UTC (rev 185)
+++ pkg.pdf	2012-10-31 12:23:42 UTC (rev 186)
@@ -1,29 +1,35 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adephylo -r 186

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